Performs fastq alignment to a fasta reference using using gem3-mapper
meta{:bash}
:map
Groovy Map containing reference/index information e.g. [ id:‘test’ ]
gem{:bash}
:file
GEM3 genome index files
*.{gem}
meta2{:bash}
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
fastq{:bash}
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
*.{fastq,fq,fastq.gz,fq.gz}
sort_bam{:bash}
:boolean
use samtools sort (true) or samtools view (false)
true or false
bam{:bash}
*.bam{:bash}
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
The GEM indexer (v3).
